Proteomic Analysis of Leishmania Strains

The protein data of L. donovani 9044 and DD8 strains was generated by using liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) in our previous studies (26 (link)). Proteomic data was not employed for immunoinformatics analysis in previous studies and it can be retrieved from ProteomeXchange Consortium via the accession number PXD017089. In brief, L. 9044 and L. DD8 were cultured and collected to incubate in lysis buffer (8 M urea and 1% protease inhibitor cocktail) at 4°C for 3 min. Lysis samples were sonicated on ice three times using a high-intensity ultrasonic processor (Scientz, Ningbo, China) and the supernatant was collected by centrifugation for an insolution reduction, alkylation, and digestion approach. The processed samples were dissolved in 1.0% (v/v) formic acid, and then subjected to liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) analysis using a QExactiveTM Plus Orbitrap mass spectrometer (Thermo Fisher Scientific) coupled online to the EASY-nLC 1000 UPLC system. Perseus software v.1.6.15.0 was employed to determine differentially expressed proteins (Fold change ≥ 3, q-value < 0.01) between L. 9044 and L. DD8.

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Zhang J., Li J., Hu K., Zhou Q., Chen X., He J., Yin S., Chi Y., Liao X., Xiao Y., Qin H., Zheng Z, & Chen J. (2022). Screening Novel Vaccine Candidates for Leishmania Donovani by Combining Differential Proteomics and Immunoinformatics Analysis. Frontiers in Immunology, 13, 902066.

Publication 2022

high-intensity ultrasonic processor QExactiveTM Plus Orbitrap mass spectrometer EASY-nLC 1000 UPLC system

Alkylation Buffer Centrifugation Digestion Formic acid Liquid chromatography Mass spectrometry mass spectrometry Protease inhibitor Proteins Strains Ultrasonic Urea

Corresponding Organization : Sichuan University

Other organizations : Guangzhou University of Chinese Medicine, First Affiliated Hospital of Guangzhou University of Chinese Medicine

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Variable analysis

independent variables

L. donovani 9044 strain
L. donovani DD8 strain

dependent variables

Differentially expressed proteins between L. donovani 9044 and L. donovani DD8 strains (Fold change ≥ 3, q-value < 0.01)

control variables

Lysis buffer composition (8 M urea and 1% protease inhibitor cocktail)
Sonication parameters (3 times on ice using a high-intensity ultrasonic processor)
Separation and analysis method (LC-MS/MS using a QExactive Plus Orbitrap mass spectrometer coupled to an EASY-nLC 1000 UPLC system)
Data analysis software (Perseus v.1.6.15.0)

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